Program Director/Principal Investigator (Last, First, Middle): Strausberg, Robert L. 1U54 AI084844-01 Human Microbiome Project (U54) Revised Scope Summary The overall objective of the Human Microbiome Project (HMP) is to define the core dataset of microbial species that is associated with the human body. The JCVI is proposing to sequence 110 reference genomes of which 15 will be "finished" in accordance with HMP guidelines. In addition, we will generate 16S rRNA gene sequence from approximately 3300 human microbiome samples obtained from a consented group of individuals collected as a result of the NIH Roadmap efforts. The JCVI team has substantial experience with human microbial genomics and metagenomics that will be invaluable to the success of this study. In addition to these major commitments, we will use new technologies to further investigate the microbial species associated with the human body through the sequencing of viral and phage genomes. Finally, we will use cutting edge technologies to generate the genomes of 20 previously uncultured microbial species. The success of our proposed study will be dependent on having access to the appropriate samples, both nucleic acids and cellular materials. This is particularly relevant to our single cell applications for uncultured species, and phage induction analyses where viable, intact fresh samples will be necessary. As proposed, the Specific Aims that we are presenting are our minimum possible based on the current state of the art, which will continue to evolve rapidly. We anticipate that current goals will be substantially exceeded as "next gen" technologies evolve and newer technologies emerge. Towards that end, we will continue to incorporate new technologies as appropriate, Adoption of these new sequencing technologies will result in greater than ten-fold increase in sequence output at an overall lower cost per unit of sequence. The incorporation of the relevant new technologies will be coordinated with the other HMP centers to ensure the generation of optimal community resources that are not only well understood but also produced cost-effectively. Additionally we also anticipate a significant reduction in library preparation costs in the coming years due to the implementation of an automated DNA shearing strategy, and more cost efficient bar- coding and multiplexing of samples for library construction and subsequent sequencing. These improvements will have a significant impact on the sequencing production costs, as well as on the quality and quantity of data generated. The resulting throughput will depend on choices made by the HMP as a whole, which will most likely reflect combined approaches and technologies. All data will be rapidly released to the DACC and the entire scientific community as a whole, in accordance with NIH policies.